Struther Arnott

Optimised parameters for A-DNA and B-DNA.

Abstract Atomic coordinates and other stereochemical parameters are presented for the A and B conformations of DNA. The molecular structures presented have the most probable values of bond-lengths, bond-angles and furanose ring conformations as defined by accurate X-ray crystallographic analyses of relevant monomers. Conformation-angles have values that provide the best (least-squares) fit with the X-ray diffraction data observed from the polymers themselves. The major difference between A- and B-DNA is in the conformation of the furanose ring that is (C3- endo ) for A and (C3- exo ) for B.

The agarose double helix and its function in agarose gel structure.

Abstract Agarose and eight different derivatives carrying O-methyl, O-sulphate, O-hydroxyethyl or O-carboxyethylidene substituents in various positions were studied by optical rotation, X-ray diffraction and computerised molecular model building methods. All samples showed essentially the same order-disorder transition during gel-sol interconversion. In addition, all the samples that could be made into oriented films or fibres gave X-ray diffraction diagrams corresponding to a common molecular structure. A double helix model for this structure is proposed that has the 0.95 nm axial periodicity observed and a calculated cylindrically averaged Fourier transform in good agreement with the observed (continuous) layer line intensities. Each chain in the double helix forms a lefthanded 3-fold helix of pitch 1.90 nm and is translated axially relative to its partner by exactly half this distance. This model accounts for the sign and magnitude of the optical rotation shift that accompanies the sol-gel transitions and is sterically accessible to each of the various substituted forms. The relationship between agarose gel properties and the double helix is discussed and the structure compared with i-carrageenan.

Structures for the polynucleotide complexes poly(dA) · poly(dT) and poly(dT) · poly(dA) · poly(dT)

X-ray diffraction analyses of fibers of polydeoxyadenylic acid · polydeoxythymidylic acid show that this molecule exists as a 10-fold double-helix with axial rise per nucleotide h = 3.24 to 3.29 A. The structure is very similar to B-DNA (h = 3.37 A) in having C3-exo furanose rings and base-pairs positioned centrally on the helix axis, but distinctive enough to have two packing modes, neither of which has been observed for B-DNA. Although the triple-stranded poly(dT) · poly(dA) · poly(dT) also has a large value of h(3.26 A), each of the chains is a 12-fold helix of the A-genus with C3-endo furanose rings and bases displaced several Angstrom units from the helix axis.

Polymorphism of DNA double helices

Abstract Native DNA duplexes in fibers exist usually in one of three well-known ( A , B and C ) forms depending on relative humidity, type of cations and the amount of retained salt. To determine the precise influence of these factors and the effect of base composition, as well as base sequence, on DNA secondary structure, X-ray diffraction methods have been used to study all four synthetic DNA duplexes with repeated dinucleotide sequences, eight of the 12 with repeated trinucleotide sequences and seven analogues in which guanine was replaced with hypoxanthine. The results indicate that there are at least six additional allomorphs denoted by B ′, C ′, C ″, D , E and S . The B ′ form ( h = 0.329 nm) observed for poly(dA) · poly(dT), poly(dI) · poly(dC) and poly[d(A-I)] · poly[d(C-T)] is a minor variant of the traditional B form ( h = 0.338 nm) of native DNA. The two C -like forms C ′ for poly[d(A-G-C)] · poly-[d(G-C-T)] and poly[d(G-G-T)] · poly[d(A-C-C)] and C ″ for poly[d(A-G)] · poly-[d(C-T)] have, respectively, 9 1 and 9 2 symmetries which reflect repetition of trinucleotide and dinucleotide sequences, respectively. Although isocompositional with poly(dA) · poly(dT), the existence of the rather different D form (8 1 ) for poly[d(A-T)] · poly[d(A-T)] or for poly[d(A-A-T)] · poly[d(A-T-T)] is a clear demonstration of the sequence effect. The I · C pair generally mimics an A · T pair, but poly[d(I-I-T)] · poly[d(A-C-C)] provides a new ( E ) form with approximately 15 2 screw symmetry and with 〈 h 〉 = 0.325 nm and 〈 t 〉 = 48 dg per nucleotide. The S form (6 5 ) observed for poly[d(G-C)] · poly[d(G-C)] and poly[d(A-C)] · poly[d(G-T)] is an unusual left-handed polydinucleotide helix and is accessible to any alternating purine-pyrimidine sequence. In it the two nucleotides have quite different conformations and involve syn purine and anti pyrimidine nucleosides.

Refinement of the structure of B-DNA and implications for the analysis of X-ray diffraction data from fibers of biopolymers

Abstract The molecular structure of the B form of DNA has been refined using the 3 A resolution X-ray diffraction intensities (from crystalline fibers of its lithium salt) and supplementary stereochemical data. Atomic positions have been determined with a precision of a few tenths of an Angstrom unit. The best model is similar to earlier ones but unlike them has no undesirable stereoehemical features, apparently as a result of having the furanose rings in a standard C3-exo conformation. The correctness of the base-pairing scheme has also been investigated. Alternatives to the Watson-Crick scheme can be rejected decisively. The strategy used to test alternative molecular models is of general application.

Structural details of a double-helix observed for DNAs containing alternating purine and pyrimidine sequences☆

Abstract Double-stranded DNA molecules in which purine and pyrimidine nucleotide residues alternate along each chain can assume a novel, right-handed, 8-fold helical form with an axial rise per residue of 3.03 A. The furanose rings have the standard C3-exo conformation. The bases are positioned unusually with respect to the helix axis even though they connect the two antiparallel chains through purinepyrimidine hydrogen bonds of the Watson & Crick (1953) type. The molecules assume an unprecedentedly dense packing in which each has four nearest neighbors with center-to-center distances of only 17 A. The molecular geometry also supports assignment of a structural rather than transcriptional role to satellite DNA in biological systems.

Optimised parameters for RNA double-helices

Abstract Atomic coordinates, obtained by analysis of the X-ray fiber diffraction data from synthetic RNA double-helices, are presented for A-RNA and A′-RNA. (A′-RNA is produced by increasing the salt content in fibers of A-RNA which is the conformation already observed for viral RNA double-helices.) The most probable values of bond-lengths and bond-angles (derived from accurate X-ray diffraction analyses of monomer crystal structures) were assigned to the polymer models which also have ribose rings in the standard C3- endo conformation. Conformation-angles have the experimental values which provide the (least-squares) best fit with the X-ray diffraction data from highly crystalline fibers of poly(A)·poly(U) (for A-RNA) and poly(I)·poly(C) (for A′-RNA). Both models are right-handed, anti-parallel, double-helices with Watson-Crick base-pairs and similar overall conformations. However, A-RNA is an eleven-fold helix whereas the A′-RNA helix is twelve-fold.

Structures of synthetic polynucleotides in the A-RNA and A′-RNA conformations: X-ray diffraction analyses of the molecular conformations of polyadenylic acid · polyuridylic acid and polyinosinic acid · polycytidylic acid

Abstract X-ray dinraction patterns snow that syntnetic RNA A aoubie-helices, poly(A) · poly(U) and poly(I) · poly(C), are 11-fold and can exist in fibers in a crystalline form isomorphous with · -A-RNA from reovirus. The data from poly(A) · poly(U) were used to refine molecular parameters (and calculate their estimated standard deviations) for A -RNA; the values of these parameters are very similar to those obtained from independent refinements using data from α- and β- A -RNA (reovirus), but for the more numerous poly (A) · poly(U) data the parameters are defined more precisely. Poly(I) · poly(C) and poly(A) · poly(U) can undergo a salt-induced transition to the 12-fold helices of A ′-RNA. Molecular parameters of A ′-RNA, with their estimated standard deviations, were obtained from a refinement using X-ray diffraction data from poly(I) · poly(C). The reported structure of the synthetic DNA-RNA hybrid poly(I) · poly(dC) is not significantly different from A ′-RNA. A ′-RNA and A ′-RNA are very similar to each other, and to A -DNA, in having antiparallel polynucleotide chains, C3- endo puckered furanose rings and Watson-Crick base pairs about 4 A from the helix axis. The most obvious difference between these molecules is in the “tilt” of the base pairs. Structural similarities between poly(A) · poly(U) and poly(I) · poly(C) are consistent with their comparable ability to induce Interferon; the tendency of poly(A) · poly(U) to form a triple helix under conditions when poly(I) · poly(C) merely undergoes the A to A ′ transition may explain why it has sometimes been found to be less effective. The homopolymer sequences of poly(A) · poly(U) and poly(I) · poly(C) may help to stabilize A -type conformations. Since homopolymer stretches in DNA appear to act as control sites for RNA transcription, the possible enhanced stability of their A conformations is consistent with a suggestion that DNA might adopt the A conformation during transcription.

i-Carrageenan: Molecular structure and packing of polysaccharide double helices in oriented fibres of divalent cation salts☆

Abstract The Ca2+ and Sr2+ salts of i-carrageenan have isomorphous crystal structures with trigonal unit cells of dimensions a = b = 1.373 nm, c = 1.328 nm, γ = 120 °. Two kinds of fibre diffraction pattern were found for the Mg2+ salt: one resembling the Ca2+ and Sr2+ patterns and one with additional layer lines interleaved midway between those in the usual kind of pattern. Specimens of this second type convert to the first type on storage at 92% relative humidity. These Mg2+ i-carrageenate diffraction patterns provide direct evidence for the double-helical nature of the carrageenan molecule. A molecular model has been derived that consists of two, identical, righthanded, 3-fold helical polysaccharide chains of pitch 2.656 nm. One chain is translated axially 1.32 nm relative to the other. A packing arrangement with up-pointing and down-pointing double helices distributed randomly among the molecular sites explains the presence of both Bragg reflections and layer line streaks. The space group of our statistical crystal structure is P3212. The divalent cations were found by Fourier difference syntheses to be at ( 2 3 , 1 3 , 1 6 ) and symmetry-related positions. The co-ordination of each cation to sulphate groups on two different helices leads to a continuous set of cation-sulphate-cation-… interactions that accounts for the high crystallinity of these salts. The structure of the Ca2+ salt has been refined by constrained linked-atom least-squares methods. The structural isomorphism of the Sr2+ salt was confirmed by an independent refinement.

Cation interactions in gellan: An x-ray study of the potassium salt

Gellan belongs to a new generation of nonsulfated, microbial, texturing polysaccharides of potential interest to the food industry. The influence of monovalent cations on its molecular geometry has been investigated by X-ray diffraction analysis of oriented fibers of the potassium salt. The molecule forms a parallel, half-staggered, double helix in which each polysaccharide chain is a left-handed, 3-fold helix of pitch 5.63 nm. The potassium ion is coordinated to the carboxylate group, which is in turn involved in interchain hydrogen-bonds to stabilize the duplex. There are two such duplexes, packed antiparallel to each other, cross-linked by a network of duplex-water-duplex interactions, in the trigonal unit cell, a = b = 1.575 nm, and c = 2.815 nm. The present study not only confirms the correctness of the basic structure of gellan reported previously for the lithium salt but also furnishes a clear insight into the critical interactions taking place between the polymer chains, cations, and water molecules which are of importance for industrial utilization.